Production at the Mitsubishi Motors Corp. and Daihatsu Motor Co. factories in Osaka and Kyoto prefectures was also halted as a result of the quake.
The Japan Meteorological Agency warned residents of Osaka and surrounding prefectures June 18 to brace for strong aftershocks over the coming week following the magnitude-6.1 quake that rocked the region around the morning commute.
The epicenter of the quake was in the northern part of Osaka Prefecture, the Japan Meteorological Agency said, and no tsunami warning was issued.
Japanese media reported one of the quake's victims is a 9-year-old girl found at a school in Takatsuki City.
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"The government has united to respond (to the disaster) under the policy to put top priority on people's lives", Prime Minister Shinzo Abe said as the government set up an emergency response team.
The JMA also said it is unlikely that another fault zone responsible for the 1995 Great Hanshin Earthquake that leveled the port city of Kobe had any influence on the June 18 quake based on the distance between the two points.
The morning commute was disrupted as train and subway service in the Osaka area including the bullet train were suspended to check for damage to equipment.
Live footage showed burst water mains and a house on fire after the quake hit Osaka, which will host next year's Group of 20 summit, just before 8 a.m. (2300 GMT Sunday) as commuters were heading to work.
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The quake struck with a magnitude of 5.9 at 7:58 a.m. local time, at a depth of 10 kilometers (6.2 miles).
Kepco said its Fukui nuclear plants were operating normally.
The area north of Osaka was the hardest hit, the agency said.
In a quake with an intensity of lower 6, it is hard to remain standing and unsecured furniture may move or topple over, according to the agency. Power was quickly restored to more than 170,000 homes that had earlier been cut off, regional utility Kansai Electric Power Co. said.
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Osaka prefecture, which includes the city and surrounding areas, has a population of 8.8 million. In 1995, a magnitude 6.9 natural disaster killed more than 6000 people when it struck in neighbouring Kobe.